Hello, Does anyone here have experience with using the CRISPR-DAV pipeline for detecting and quantifying indels after a CRISPR knockout? I've gotten pretty far ahead with my analysis but I'm getting stuck on analysis with the ABRA realigner.
Briefly, the CRISPR-DAV pipeline uses BWA (burrows-wheeler alignment) and then realigns inputs from the BWA alignment using the ABRA realigner software.
After feeding the program all the input files in the correct format, I keep getting an error saying that ABRA realignment is failing on my samples.
Has anyone encountered this error before and has any ideas on what I could do to fix it?
Please let me know!
Thank you, Graduate student in distress
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